[phenixbb] query re local grid search in phenix.real_space_refine

Oliver Clarke olibclarke at gmail.com
Sat Feb 10 09:41:35 PST 2018

Hi all,

Related to the last message - when using local_grid_search, does phenix attempt to torsion-angle search every residue, or just outliers? 

It would seem like maybe using EMRinger or similar to identify residues where there is strong sidechain density, but in a non-rotameric position or with an incorrectly fit rotamer might be one way to make it more efficient if it is the former. 

I don’t want phenix trying to do a local grid search on residues with no sidechain density - these may be in an area of the map with poor local resolution, perhaps where I have docked a crystal structure, or carefully manually adjusted rotamers - local grid search in these regions is likely to make things worse if it is not focused on residues with clear sidechain density.


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